Last updated: 2020-11-21
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| absolute | relative |
|---|---|
| /project2/xinhe/xsun/website/factor_analysis/output/sum_sep_tog_pval_pliercanon_wgpc_ldcl_d1k_ageco_adp.rdata | output/sum_sep_tog_pval_pliercanon_wgpc_ldcl_d1k_ageco_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/info_pval5e8_pliercanon_ld_d1k_ageco_adp.rdata | output/info_pval5e8_pliercanon_ld_d1k_ageco_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/lv74top025_pliercanon_adp.rdata | output/lv74top025_pliercanon_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/lv84top025_pliercanon_adp.rdata | output/lv84top025_pliercanon_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/lv121top025_pliercanon_adp.rdata | output/lv121top025_pliercanon_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/lv29top025_pliercanon_adp.rdata | output/lv29top025_pliercanon_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/lv35top025_pliercanon_adp.rdata | output/lv35top025_pliercanon_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/lv104top025_pliercanon_adp.rdata | output/lv104top025_pliercanon_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/eo_74_26498530.coloc.results_adp.rdata | output/eo_74_26498530.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/eo_74_26521207.coloc.results_adp.rdata | output/eo_74_26521207.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/eo_74_27970706.coloc.results_adp.rdata | output/eo_74_27970706.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/eo_74_28986516.coloc.results_adp.rdata | output/eo_74_28986516.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/eo_74_30331468.coloc.results_adp.rdata | output/eo_74_30331468.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/eo_84_132280681.coloc.results_adp.rdata | output/eo_84_132280681.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/eo_84_132395414.coloc.results_adp.rdata | output/eo_84_132395414.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/eo_121_233205886.coloc.results_adp.rdata | output/eo_121_233205886.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/eo_121_23520972.coloc.results_adp.rdata | output/eo_121_23520972.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/eo_121_96350497.coloc.results_adp.rdata | output/eo_121_96350497.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/EUR.UC_29_206798727.coloc.results_adp.rdata | output/EUR.UC_29_206798727.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/EUR.UC_29_32836793.coloc.results_adp.rdata | output/EUR.UC_29_32836793.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/gran_74_157050529.coloc.results_adp.rdata | output/gran_74_157050529.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/gran_74_26463347.coloc.results_adp.rdata | output/gran_74_26463347.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/gran_74_27873148.coloc.results_adp.rdata | output/gran_74_27873148.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/gran_74_31276269.coloc.results_adp.rdata | output/gran_74_31276269.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/LDL_35_20816003.coloc.results_adp.rdata | output/LDL_35_20816003.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/LDL_35_45149969.coloc.results_adp.rdata | output/LDL_35_45149969.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/lymph_74_26463347.coloc.results_adp.rdata | output/lymph_74_26463347.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/lymph_74_27873148.coloc.results_adp.rdata | output/lymph_74_27873148.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/lymph_74_28894720.coloc.results_adp.rdata | output/lymph_74_28894720.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/lymph_74_30331468.coloc.results_adp.rdata | output/lymph_74_30331468.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/neut_74_157050529.coloc.results_adp.rdata | output/neut_74_157050529.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/neut_74_26463347.coloc.results_adp.rdata | output/neut_74_26463347.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/neut_74_27873148.coloc.results_adp.rdata | output/neut_74_27873148.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/neut_74_28894720.coloc.results_adp.rdata | output/neut_74_28894720.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/neut_74_31276269.coloc.results_adp.rdata | output/neut_74_31276269.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/myeloid_wbc_74_157050529.coloc.results_adp.rdata | output/myeloid_wbc_74_157050529.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/myeloid_wbc_74_26463347.coloc.results_adp.rdata | output/myeloid_wbc_74_26463347.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/myeloid_wbc_74_27873148.coloc.results_adp.rdata | output/myeloid_wbc_74_27873148.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/myeloid_wbc_74_28894720.coloc.results_adp.rdata | output/myeloid_wbc_74_28894720.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/myeloid_wbc_74_30331468.coloc.results_adp.rdata | output/myeloid_wbc_74_30331468.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/myeloid_wbc_74_5280229.coloc.results_adp.rdata | output/myeloid_wbc_74_5280229.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/rbc_104_31149298.coloc.results_adp.rdata | output/rbc_104_31149298.coloc.results_adp.rdata |
| /project2/xinhe/xsun/website/factor_analysis/output/rbc_104_47092874.coloc.results_adp.rdata | output/rbc_104_47092874.coloc.results_adp.rdata |
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The analysis in this part is the same with PLIER-Canonical. But in this part, I used Adipose Subcutaneous expression data. It contains 581 samples.
This part is the same with PLIER-Canonical.
After filtering by ‘pval < 5e-8’ and LD Clumping, for each trait, I got :
platelet count trait contains 691 SNPs with pval<5e-8.
white blood cell count trait contains 367 SNPs with pval<5e-8.
myeloid white cell count trait contains 317 SNPs with pval<5e-8.
lymphocyte count trait contains 446 SNPs with pval<5e-8.
red blood cell count trait contains 462 SNPs with pval<5e-8.
granulocyte count trait contains 308 SNPs with pval<5e-8.
eosinophil count trait contains 496 SNPs with pval<5e-8.
neutrophil count trait contains 311 SNPs with pval<5e-8.
IBD trait contains 118 SNPs with pval<5e-8.
Ulcerative colitist trait contains 75 SNPs with pval<5e-8.
Crohn’s disease trait contains 97 SNPs with pval<5e-8.
BMI trait contains 102 SNPs with pval<5e-8.
T2D contains 14 SNPs with pval<5e-8. T2D_2 contains 4 SNPs with pval<5e-8.
Asthma trait contains 192 SNPs with pval<5e-8. Asthma_2 trait contains 110 SNPs with pval<5e-8.
HDL trait contains 225 SNPs with pval<5e-8.
LDL trait contains 203 SNPs with pval<5e-8.
WHR trait contains 37 SNPs with pval<5e-8.
I used ‘qvalue’ R package to compute the fdr from p-values for each SNP and made a table to show the number of SNPs that pass the threshold. The thresholds are ‘fdr < 0.1’,‘fdr < 0.2’,‘pval < 5e-8’. The ‘num_significant_pairs’ indicates the number of significant pairs under each threshold. If a trait~factor pair has as least 1 significant SNP, we named it as ‘significant pair’.
For each trait, I made a table to show the info of snps with fdr>0.2 in the factor ~ SNP + genotype pcs association test. For each trait,The LVs have more than one significant SNPs with FDR<0.2 are included.
The suffix ’_assoc’ here means that results are from factor ~ SNP + genotype pcs association test. The suffix ’_gwas’ here means results are from original GWAS results files. For EUR.CD, EUR.IBD, EUR.UC, the effectsize_gwas here means ‘ln(OR)’, for others, it means ‘beta’.
‘snp_ld’ here means the snps that in LD with the snp in each line.’ld_r2’ means the LD r-squared which is corresponding to the ‘snp_ld’ column. ‘cis-eqtl’ column indicates whether the snp is a cis-eqtl according to GTEx data. ‘cis_gene_hgnc’ and ‘cis_gene_hgnc’ is the genes that the snp influence when it act as cis-eqtl. ‘func’ and ‘func_gene’ are obtained from ANNOVAR, which indicating the snp function within the genes.
Eocinophil/granulocyte count/neutrophil count/lymphocyte count/myeloid white cell count - LV74
Eocinophil - LV84
Eocinophil - LV121
Ulcerative colitist - LV29
LDL - LV35
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Red Blood Cell Count - LV104
For each trait, I made a plot of association with LV(indicating by beta in GWAS) vs association with trait(indicating by ln(odds ratio) or beta in GWAS) to show if the variants have the correlated effect direction. The effect sizes of Catalog GWAS and factor association tests are harmonized by TwoSampleMR R package to make the effect alleles in these two analysis identical. The LVs have more than one significant SNPs with FDR<0.2 are included in the plotting.Besides, for each plots, I fitted the points with intercept = 0. The pvalues and r-squared are shown on the plots.
None of the LVs have >1 SNPs at FDR<0.2.
None of the LVs have >1 SNPs at FDR<0.2.
None of the LVs have >1 SNPs at FDR<0.2.
None of the LVs have >1 SNPs at FDR<0.2.
None of the LVs have >1 SNPs at FDR<0.2.
None of the LVs have >1 SNPs at FDR<0.2.
For some promising trait-factor pairs, I did resampling. I resampled the SNPs without replacement, I fitted the points with intercept = 0 again and recorded the pvalues and r-squared. The resampling was repeated 1000 times. The following plots are the resampling results.
I made a histogram to show the pvalues/rsquared distribution from resampling. The red line in the plots are the pvalue/rsquared in the origin analysis. The p_mean/r_mean values in the plots are the mean values of the resampling. The ‘prob of getting more extreme values’ is computed by: (number of more extreme values)/(times of resampling)
For some promising trait-factor pairs , I relaxed the fdr threshold of the SNPs that used to make effect size plots(from 0.2 to 0.3/0.5)
To check if the effect size correlation is due to reverse causality: i.e. trait -> LV (trait causally affect LV), instead of LV -> trait (which is what we like to see). I used all SNPs associated with traits(pval<5E-8). The x-axis is the effects of these SNPs on trait, and y-axis is the effects on LV.
Some pair show p < 0.05, the result may be driven by the possible causal effect of LV -> trait. To test this, I removed the SNPs that are associated with LVs at FDR < 0.2 and made the plots again.
The colocalization analysis was performed using the approximate Bayes factor test implemented in the Coloc package. Coloc computes five posterior probabilities (PP0, PP1, PP2, PP3 and PP4), each corresponding to a hypothesis: H0, no association with either trait; H1, association with trait 1 but not with trait 2; H2, association with trait 2 but not with trait 1; H3, association with trait 1 and trait 2, two independent SNPs; H4, association with trait 1 and trait 2, one shared SNP. We ran Coloc with the default parameters and used PP4 to assess evidence of colocalization. We visualized the colocalization of factor - QTLs and GWAS associations using the LocusCompareR package.
Chromosome selection: I first sorted the SNPs by their pvalues from factor association tests, then I selected the first two SNPs and chose their chromosome to do the colocalization test adn visualization.
LV74
| note | ||
|---|---|---|
| nsnps | 654 | NA |
| PP.H0.abf | 4.32951012214208e-15 | no association with either trait |
| PP.H1.abf | 1.47039883050559e-14 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.012147306446318 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.0403074343772307 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.947545259176435 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 551 | NA |
| PP.H0.abf | 4.51503740879928e-15 | no association with either trait |
| PP.H1.abf | 1.49802568801237e-14 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.0109205471062468 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.035279033577639 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.953800419316093 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 587 | NA |
| PP.H0.abf | 1.30154749414775e-21 | no association with either trait |
| PP.H1.abf | 9.73567901978272e-22 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.0301083403492439 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.0215729599148834 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.948318699735872 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 100 | NA |
| PP.H0.abf | 0.895363538820831 | no association with either trait |
| PP.H1.abf | 0.0964494552470313 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.00366956720683393 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.00039116317140931 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.00412627555389428 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 151 | NA |
| PP.H0.abf | 0.909990082714903 | no association with either trait |
| PP.H1.abf | 0.0806086328367058 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.00549203403761318 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.000483068521375786 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.00342618188940235 | association with trait 1 and trait 2, one shared SNP |
lv84
| note | ||
|---|---|---|
| nsnps | 633 | NA |
| PP.H0.abf | 0.520867968468262 | no association with either trait |
| PP.H1.abf | 0.219558425612122 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.0163221224603899 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.00664356080914982 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.236607922650077 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 670 | NA |
| PP.H0.abf | 9.52195421752099e-90 | no association with either trait |
| PP.H1.abf | 1.96819913996693e-90 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.693469246408423 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.143177555947148 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.163353197644415 | association with trait 1 and trait 2, one shared SNP |
lv121
| note | ||
|---|---|---|
| nsnps | 836 | NA |
| PP.H0.abf | 0.803428972151636 | no association with either trait |
| PP.H1.abf | 0.128323078245838 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.0528939231585165 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.00844126532987787 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.00691276111413178 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 583 | NA |
| PP.H0.abf | 4.52990830876848e-06 | no association with either trait |
| PP.H1.abf | 9.21861694069134e-07 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.0916212125783412 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.0177548110256025 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.890618524626053 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 281 | NA |
| PP.H0.abf | 2.77707888116324e-29 | no association with either trait |
| PP.H1.abf | 2.10073251325066e-30 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.395264611924459 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.029324540040624 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.575410848034918 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 466 | NA |
| PP.H0.abf | 6.36858252526649e-12 | no association with either trait |
| PP.H1.abf | 1.25749787143433e-12 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.76638668186091 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.151243237668553 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.0823700804629126 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 484 | NA |
| PP.H0.abf | 2.39875722879442e-07 | no association with either trait |
| PP.H1.abf | 1.58234762077974e-08 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.871084985071383 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.0573898654077472 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.0715248938216703 | association with trait 1 and trait 2, one shared SNP |
lv74
| note | ||
|---|---|---|
| nsnps | 807 | NA |
| PP.H0.abf | 0.000243730196779536 | no association with either trait |
| PP.H1.abf | 0.000165248082383001 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.115588213386481 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.077561897771207 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.80644091056315 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 786 | NA |
| PP.H0.abf | 3.19604103017961e-12 | no association with either trait |
| PP.H1.abf | 1.03593792505706e-11 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.014003650916366 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.0444487115504494 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.94154763751963 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 510 | NA |
| PP.H0.abf | 1.82259340012189e-17 | no association with either trait |
| PP.H1.abf | 1.92483992741527e-17 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.0297496892787095 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.030478859686348 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.939771451034946 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 510 | NA |
| PP.H0.abf | 1.82259340012189e-17 | no association with either trait |
| PP.H1.abf | 1.92483992741527e-17 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.0297496892787095 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.030478859686348 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.939771451034946 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 172 | NA |
| PP.H0.abf | 1.69067886793852e-46 | no association with either trait |
| PP.H1.abf | 5.78786302442303e-48 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.249934649969975 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.00781400109211381 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.742251348937904 | association with trait 1 and trait 2, one shared SNP |
lv35
| note | ||
|---|---|---|
| nsnps | 150 | NA |
| PP.H0.abf | 1.14243004211355e-21 | no association with either trait |
| PP.H1.abf | 4.88169641330046e-23 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.914923549379037 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.039049399756932 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.04602705086403 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 80 | NA |
| PP.H0.abf | 2.38940663497786e-14 | no association with either trait |
| PP.H1.abf | 7.2663269498117e-15 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.594951780945732 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.180704012500906 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.224344206553332 | association with trait 1 and trait 2, one shared SNP |
lv74
| note | ||
|---|---|---|
| nsnps | 786 | NA |
| PP.H0.abf | 1.7445088448985e-35 | no association with either trait |
| PP.H1.abf | 5.65450460730246e-35 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.0120008783933029 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.0379485898305526 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.950050531776139 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 510 | NA |
| PP.H0.abf | 1.07493786039491e-42 | no association with either trait |
| PP.H1.abf | 1.13524130672266e-42 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.0295868451797152 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.030306544960568 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.940106609859711 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 56 | NA |
| PP.H0.abf | 3.43436637262214e-46 | no association with either trait |
| PP.H1.abf | 2.92432501543514e-47 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.0605874640743969 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.00422376684575926 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.935188769079843 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 151 | NA |
| PP.H0.abf | 0.909367744368301 | no association with either trait |
| PP.H1.abf | 0.0805535049356063 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.00659955289120895 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.000581703311602042 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.00289749449328192 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 807 | NA |
| PP.H0.abf | 0.000214294779531181 | no association with either trait |
| PP.H1.abf | 0.000145290989176229 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.117951543823456 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.079168146384457 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.80252072402338 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 786 | NA |
| PP.H0.abf | 2.82528454381721e-09 | no association with either trait |
| PP.H1.abf | 9.15764028177483e-09 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.0153647114415028 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.048866117423375 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.935769159152199 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 510 | NA |
| PP.H0.abf | 1.44966591128561e-13 | no association with either trait |
| PP.H1.abf | 1.53099140338639e-13 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.0296802594352 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.0304053919677193 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.939914348596783 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 56 | NA |
| PP.H0.abf | 1.5259694149023e-14 | no association with either trait |
| PP.H1.abf | 1.29934609433665e-15 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.0596791572833565 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.00414543889146503 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.936175403825163 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 172 | NA |
| PP.H0.abf | 9.90493571701678e-41 | no association with either trait |
| PP.H1.abf | 3.39085158529905e-42 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.262118676406559 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.00824372229545226 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.729637601297983 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 807 | NA |
| PP.H0.abf | 0.000126242289634006 | no association with either trait |
| PP.H1.abf | 8.5591759056958e-05 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.112136433902647 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.0752156101050989 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.812436121943563 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 786 | NA |
| PP.H0.abf | 1.06923834059985e-14 | no association with either trait |
| PP.H1.abf | 3.46573944919043e-14 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.0134520292367394 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.0426583893747474 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.943889581388469 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 510 | NA |
| PP.H0.abf | 2.39167301496117e-20 | no association with either trait |
| PP.H1.abf | 2.52584460813423e-20 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.0296523673059772 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.0303758776983773 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.939971754995643 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 56 | NA |
| PP.H0.abf | 1.68997869196331e-22 | no association with either trait |
| PP.H1.abf | 1.43899818139885e-23 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.0589076369402022 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.00407890673429991 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.937013456325495 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 151 | NA |
| PP.H0.abf | 0.908607813893165 | no association with either trait |
| PP.H1.abf | 0.0804861888650081 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.00680067114563086 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.000598909823017954 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.00350641627317808 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 740 | NA |
| PP.H0.abf | 0.696244518692255 | no association with either trait |
| PP.H1.abf | 0.241303199421013 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.0295609541707098 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.0102225146358729 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.0226688130801494 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 1 | NA |
| PP.H0.abf | 0.999890377109835 | no association with either trait |
| PP.H1.abf | 5.59464824756157e-05 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 5.08322124194453e-05 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 2.84419527022698e-06 | association with trait 1 and trait 2, one shared SNP |
| note | ||
|---|---|---|
| nsnps | 434 | NA |
| PP.H0.abf | 0.884468683582122 | no association with either trait |
| PP.H1.abf | 0.0929659932493666 | association with trait 1 but not with trait 2 |
| PP.H2.abf | 0.0163931929316615 | association with trait 2 but not with trait 1 |
| PP.H3.abf | 0.00171862555024174 | association with trait 1 and trait 2,two independent SNPs |
| PP.H4.abf | 0.00445350468660804 | association with trait 1 and trait 2, one shared SNP |
sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 rstudioapi_0.11 whisker_0.3-2 knitr_1.30
[5] magrittr_1.5 R6_2.4.1 rlang_0.4.8 highr_0.8
[9] stringr_1.4.0 tools_3.6.1 DT_0.15 xfun_0.18
[13] git2r_0.26.1 crosstalk_1.1.0.1 htmltools_0.5.0 ellipsis_0.3.1
[17] rprojroot_1.3-2 yaml_2.2.1 digest_0.6.25 tibble_3.0.3
[21] lifecycle_0.2.0 crayon_1.3.4 later_1.1.0.1 htmlwidgets_1.5.2
[25] vctrs_0.3.4 promises_1.1.1 fs_1.5.0 glue_1.4.2
[29] evaluate_0.14 rmarkdown_1.13 stringi_1.5.3 compiler_3.6.1
[33] pillar_1.4.6 backports_1.1.10 jsonlite_1.7.1 httpuv_1.5.1
[37] pkgconfig_2.0.3